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NM_001089.3(ABCA3):c.4648C>T (p.Arg1550Trp) AND Hereditary pulmonary alveolar proteinosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 11, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002335061.2

Allele description [Variation Report for NM_001089.3(ABCA3):c.4648C>T (p.Arg1550Trp)]

NM_001089.3(ABCA3):c.4648C>T (p.Arg1550Trp)

Gene:
ABCA3:ATP binding cassette subfamily A member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001089.3(ABCA3):c.4648C>T (p.Arg1550Trp)
HGVS:
  • NC_000016.10:g.2278358G>A
  • NG_011790.2:g.67370C>T
  • NM_001089.3:c.4648C>TMANE SELECT
  • NP_001080.2:p.Arg1550Trp
  • NC_000016.9:g.2328359G>A
  • NG_011790.1:g.67389C>T
  • NM_001089.2:c.4648C>T
Protein change:
R1550W
Molecular consequence:
  • NM_001089.3:c.4648C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary pulmonary alveolar proteinosis
Synonyms:
Pulmonary surfactant metabolism dysfunction
Identifiers:
MONDO: MONDO:0012580; MedGen: C3711368; OMIM: PS265120

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002640290Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Mar 11, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002640290.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.R1550W variant (also known as c.4648C>T), located in coding exon 27 of the ABCA3 gene, results from a C to T substitution at nucleotide position 4648. The arginine at codon 1550 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration was first described in a newborn with respiratory failure, tachypnea, and hypoxemia; this newborn also carried the c.288dupA alteration, phase not reported (Doan ML et al. Thorax. 2008;63(4):366-73). This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6498 samples (12996 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024